Nano-roughness evaluation for the surface of epitaxial graphene and height measurement are considered for a microstep on as-grown surface of sapphire in order to provide homogeneous graphene films on large areas of silicon carbide or sapphire substrates. To investigate dissimilar surface properties, different approaches have been used: off-specular grazing incidence X-ray scattering and in-line phase contrast imaging with synchrotron radiation. Statistical and local parameters of two types of surface morphology are measured. For the graphene surface, the dependence of the root-mean-square roughness of terrace-step nanostructure on the direction of the steps is estimated. For the vicinal face of sapphire, a surface step height of about one micron is determined directly from a phase contrast image, proving for the first time that the phase contrast imaging resolves surface morphology on a micrometer scale. Atomic force microscopy confirmed the obtained results.